Polycystic ovary syndrome is a complex endocrinopathy with heterogeneous presentation and multifactorial etiology. We have undertaken this case-control study to compare metabolic and endocrine characteristics in different phenotypic subgroups of women with PCOS and the impact of obesity on them. Women with PCOS (n = 489) were classified into 4 phenotypes according to Rotterdam criteria. Comparisons of clinical, biochemical and hormonal parameters were performed across all phenotypic groups of PCOS and with controls (n = 270) by Welch's ANOVA with subsequent Games-Howell post-hoc test. We found maximum prevalence of normoandrogenic phenotype D, which is milder form of PCOS in terms of insulin resistance, gonadotropin levels and dyslipidemia, followed by phenotype A, in our total study population. After classification of the study group into lean and obese groups, only few insulin and lipid-related traits showed marked differences between phenotypes. Further, we noted that obese women showed adverse metabolic but not androgenic traits compared to lean counterparts in the same phenotype. Metabolic syndrome frequency is increased in hyperandrogenic phenotypes with HDL-C and waist circumference being most predominant contributing factors in total, lean and obese groups. We demonstrate that in our study population there is greater occurrence of phenotype D of PCOS. Our study highlights the importance of clinicians concurrently employing Rotterdam criteria along with obesity status for ascertaining accurate PCOS status and formulating suitable therapeutic intervention.